Was just down there a month ago beginning of May at Crystal River, and yes it is too late for getting wet.
The area wasn't clear pristine backcountry I expected until you got into Three Sister Spring (being developed for conservation, but only accessible by water now).
We saw 4 manatees swimming free while kayaking open water and a large male went under my kayak three times, while a female and calf were tooling around the dock for two hours.
Just missed one off beach at John Pennekamp while snorkeling ...went nose to nose with another visitor, and another was just off dock at Moon Bay Marina at Key Largo on bay side.
HOWEVER, I really have a terrific suggestion, but you won't be getting wet...well worth the trip and spending 4 hours there with camera in hand ...there is a State Park (really a zoo) which currently has four rehab manatees and 4 permanent residents ...and an underwater observation platform (goes down 30 ft into spring) ...when we were viewing, there were 75 snook up to 30 pounds, schools of other fish large and small, and the manatees tool around at their pleasure.
Welcome to Florida State Parks
there is a inexpensive kayak/canoe rental place at Kings Bay about a mile away ...$35/day and they had singles and doubles